[phenixbb] Excluding atoms from coordinate refinement ignored
Pavel Afonine
pafonine at lbl.gov
Fri Dec 21 17:00:52 PST 2012
Hi Engin,
that's bad. Could you please send me inputs so I can reproduce this?
Pavel
On 12/21/12 4:55 PM, Engin Özkan wrote:
> Hi Phenix developers,
>
> I have an issue using 1.8.1 (1168) with excluding atoms from
> coordinate refinement. I have defined a certain residue to be excluded
> from coordinate refinement, as can be seen in the .eff file produced
> by this run.
>
> refine {
> strategy = *individual_sites individual_sites_real_space rigid_body \
> *individual_adp group_adp *tls *occupancies
> group_anomalous
> sites {
> individual = not (resseq 60 and resname PHE)
> torsion_angles = not (resseq 60 and resname PHE)
> rigid_body = None
> ...
>
> However, this gets ignored, and this residue and its NCS-related
> brethren get moved into nondescript electron density on a symmetry
> axis. This residue was just fine in an earlier version of Phenix, but
> when I switched to 1.8.1, it started moving into this density. So, I
> thought excluding it from xyz refinement, which is a dirty trick in my
> opinion, would fix this problem. Not so.
>
> I have the feeling that this is due to rotamer corrections as part of
> the torsion NCS implemented in 1.8.1 now. Sticking a zero occupancy
> dummy atom in the density did prevent this residue from moving in.
> Turning off torsion NCS also fixed it. By the way, I have "fix rotamer
> sidechains" off, as I am yet to see it improve things (at medium or
> low resolution).
>
> Thanks and happy holidays!
> Engin
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